chr1-24970252-A-C

Position:

• chr1-24970252-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000568143.1(ENSG00000261025):​n.614T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,152 control chromosomes in the GnomAD database, including 30,284 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.62 (30245 hom., cov: 31)
  • Exomes 𝑓: 0.61 (39 hom.)
• Consequence: ENST00000568143.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000568143.1	n.614T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93880 AN: 151832 Hom.: 30191 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.614 AC: 124 AN: 202 Hom.: 39 Cov.: 0 AF XY: 0.615 AC XY: 91 AN XY: 148

Gnomad4 AFR exome AF: 0.833

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.633

Gnomad4 NFE exome AF: 0.597

Gnomad4 OTH exome AF: 0.722

GnomAD4 genome AF: 0.619 AC: 93994 AN: 151950 Hom.: 30245 Cov.: 31 AF XY: 0.628 AC XY: 46635 AN XY: 74264

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.610

Alfa AF: 0.576 Hom.: 3333

Bravo AF: 0.636

Asia WGS AF: 0.720 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10751776; hg19: chr1-25296743;